Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value

Silvio Fici, Adriana Martorana, Ignazio Fontana, Francesco Mercati, Alessandro Silvestre Gristina, Mahran El Nagar, Adriana Martorana, Roberto De Michele, Francesco Carimi, Francesco Mercati

Risultato della ricerca: Article

1 Citazione (Scopus)

Abstract

Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its fower buds and fruits, used as foodand for their medicinal properties. Breeding programs and even proper taxonomic classifcation of thegenus Capparis has been hampered so far by the lack of reliable genetic information and molecularmarkers. Here, we present the frst genomic resource for C. spinosa, generated by transcriptomicapproach and de novo assembly. The sequencing efort produced nearly 80million clean readsassembled into 124,723 unitranscripts. Careful annotation and comparison with public databasesrevealed homologs to genes with a key role in important metabolic pathways linked to abiotic stresstolerance and bio-compounds production, such purine, thiamine and phenylpropanoid biosynthesis,α-linolenic acid and lipid metabolism. Additionally, a panel of genes involved in stomatal development/distribution and encoding for Stress Associated Proteins (SAPs) was also identifed. We also used thetranscriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 provedpolymorphic and represent the frst set of SSR markers for the genus Capparis. This transcriptome willbe an important contribution to future studies and breeding programs for this orphan crop, aiding to thedevelopment of improved varieties to sustain agriculture in arid conditions.
Lingua originaleEnglish
Numero di pagine16
RivistaScientific Reports
Stato di pubblicazionePublished - 2019

Fingerprint

Capparis spinosa
Capparis
transcriptomics
drought
medicinal properties
dry environmental conditions
breeding
phenylpropanoids
crops
purines
thiamin
linolenic acid
transcriptome
lipid metabolism
biochemical pathways
genes
shrubs
buds
biosynthesis
agriculture

All Science Journal Classification (ASJC) codes

  • General

Cita questo

Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value. / Fici, Silvio; Martorana, Adriana; Fontana, Ignazio; Mercati, Francesco; Gristina, Alessandro Silvestre; El Nagar, Mahran; Martorana, Adriana; De Michele, Roberto; Carimi, Francesco; Mercati, Francesco.

In: Scientific Reports, 2019.

Risultato della ricerca: Article

Fici, S, Martorana, A, Fontana, I, Mercati, F, Gristina, AS, El Nagar, M, Martorana, A, De Michele, R, Carimi, F & Mercati, F 2019, 'Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value', Scientific Reports.
Fici, Silvio ; Martorana, Adriana ; Fontana, Ignazio ; Mercati, Francesco ; Gristina, Alessandro Silvestre ; El Nagar, Mahran ; Martorana, Adriana ; De Michele, Roberto ; Carimi, Francesco ; Mercati, Francesco. / Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value. In: Scientific Reports. 2019.
@article{d4c6d2d6a0114cb58e73b6e2e15fe42d,
title = "Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value",
abstract = "Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its fower buds and fruits, used as foodand for their medicinal properties. Breeding programs and even proper taxonomic classifcation of thegenus Capparis has been hampered so far by the lack of reliable genetic information and molecularmarkers. Here, we present the frst genomic resource for C. spinosa, generated by transcriptomicapproach and de novo assembly. The sequencing efort produced nearly 80million clean readsassembled into 124,723 unitranscripts. Careful annotation and comparison with public databasesrevealed homologs to genes with a key role in important metabolic pathways linked to abiotic stresstolerance and bio-compounds production, such purine, thiamine and phenylpropanoid biosynthesis,α-linolenic acid and lipid metabolism. Additionally, a panel of genes involved in stomatal development/distribution and encoding for Stress Associated Proteins (SAPs) was also identifed. We also used thetranscriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 provedpolymorphic and represent the frst set of SSR markers for the genus Capparis. This transcriptome willbe an important contribution to future studies and breeding programs for this orphan crop, aiding to thedevelopment of improved varieties to sustain agriculture in arid conditions.",
author = "Silvio Fici and Adriana Martorana and Ignazio Fontana and Francesco Mercati and Gristina, {Alessandro Silvestre} and {El Nagar}, Mahran and Adriana Martorana and {De Michele}, Roberto and Francesco Carimi and Francesco Mercati",
year = "2019",
language = "English",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value

AU - Fici, Silvio

AU - Martorana, Adriana

AU - Fontana, Ignazio

AU - Mercati, Francesco

AU - Gristina, Alessandro Silvestre

AU - El Nagar, Mahran

AU - Martorana, Adriana

AU - De Michele, Roberto

AU - Carimi, Francesco

AU - Mercati, Francesco

PY - 2019

Y1 - 2019

N2 - Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its fower buds and fruits, used as foodand for their medicinal properties. Breeding programs and even proper taxonomic classifcation of thegenus Capparis has been hampered so far by the lack of reliable genetic information and molecularmarkers. Here, we present the frst genomic resource for C. spinosa, generated by transcriptomicapproach and de novo assembly. The sequencing efort produced nearly 80million clean readsassembled into 124,723 unitranscripts. Careful annotation and comparison with public databasesrevealed homologs to genes with a key role in important metabolic pathways linked to abiotic stresstolerance and bio-compounds production, such purine, thiamine and phenylpropanoid biosynthesis,α-linolenic acid and lipid metabolism. Additionally, a panel of genes involved in stomatal development/distribution and encoding for Stress Associated Proteins (SAPs) was also identifed. We also used thetranscriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 provedpolymorphic and represent the frst set of SSR markers for the genus Capparis. This transcriptome willbe an important contribution to future studies and breeding programs for this orphan crop, aiding to thedevelopment of improved varieties to sustain agriculture in arid conditions.

AB - Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its fower buds and fruits, used as foodand for their medicinal properties. Breeding programs and even proper taxonomic classifcation of thegenus Capparis has been hampered so far by the lack of reliable genetic information and molecularmarkers. Here, we present the frst genomic resource for C. spinosa, generated by transcriptomicapproach and de novo assembly. The sequencing efort produced nearly 80million clean readsassembled into 124,723 unitranscripts. Careful annotation and comparison with public databasesrevealed homologs to genes with a key role in important metabolic pathways linked to abiotic stresstolerance and bio-compounds production, such purine, thiamine and phenylpropanoid biosynthesis,α-linolenic acid and lipid metabolism. Additionally, a panel of genes involved in stomatal development/distribution and encoding for Stress Associated Proteins (SAPs) was also identifed. We also used thetranscriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 provedpolymorphic and represent the frst set of SSR markers for the genus Capparis. This transcriptome willbe an important contribution to future studies and breeding programs for this orphan crop, aiding to thedevelopment of improved varieties to sustain agriculture in arid conditions.

UR - http://hdl.handle.net/10447/371250

M3 - Article

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

ER -